[BioC] Limma read GenePix version 6 file

[Gordon Smyth]

Er, why are you specifying sep="," for tab-delimited file?

This file reads fine in all versions of limma using default settings.

Gordon

At 10:44 PM 17/10/2005, Ye, Bin wrote:
>Hi, Gordon,
>
>Thank you for your reply! I feel it's more likely a limma problem, see my 
>code below:
>
>RG <- read.maimages("03_122589_0693_1_Cont_PMT400_r40_g10.gpr", 
>source="genepix", sep=",")
>Error in "[.data.frame"(obj, , columns[[a]]) :
>         undefined columns selected
>
>The gpr file was generated by GenePix 6. I'm attaching the file, in case 
>you need it for debugging.
>
>BTW, my system is: R 2.1.1, limma 2.0.8 and limma 2.2.0 both used, both 
>gave the same error as above.
>
>
>Bin
>
>
>-----Original Message-----
>From: Gordon Smyth [mailto:smyth at wehi.edu.au]
>Sent: Sat 10/15/2005 6:20 AM
>To: Ye, Bin
>Cc: bioconductor at stat.math.ethz.ch; Saroj Mohapatra
>Subject: Re: [BioC] Limma read GenePix version 6 file
>
>limma has been well tested with GenePix 6 and there should be no problem.
>Specifying columns explicitly should not be required. If you believe
>there's a limma error, please give the code you used so that we can debug.
>
>BTW, the columns that Saroj specified (all medians) can now be given as
>
>     source="genepix.median"
>
>Gordon
>
> >Date: Fri, 14 Oct 2005 16:11:25 -0400
> >From: "Ye, Bin" <binye at med.wayne.edu>
> >Subject: Re: [BioC] Limma read GenePix version 6 file
> >To: "Saroj Mohapatra" <smohapat at vbi.vt.edu>
> >Cc: bioconductor at stat.math.ethz.ch
> >
> >It works! Thank you, Saroj!
> >
> >Have a good weekend!
> >
> >
> >
> >Bin
> >
> >
> >-----Original Message-----
> >From: Saroj Mohapatra [mailto:smohapat at vbi.vt.edu]
> >Sent: Fri 10/14/2005 3:19 PM
> >To: Ye, Bin
> >Cc: bioconductor at stat.math.ethz.ch
> >Subject: Re: [BioC] Limma read GenePix version 6 file
> >
> >Bin:
> >
> >Which function are you using for reading the data?
> >
> >If you are using the limma function read.maimages, then the function
> >provides some extra arguments that can force it to read specific
> >columns. The help file says:
> >
> >----
> >  > ?read.maimages()
> >
> >columns: list with fields 'Rf', 'Gf', 'Rb' and 'Gb' giving the column
> >           names to be used for red and green foreground and background
> >           or, in the case of Imagene data, a list with fields 'f' and
> >           'b'.  This argument is not usually specified by the user but,
> >           if it is, it over-rides 'source'.
> >-----
> >
> >Something like this might work:
> >
> >myRG = read.maimages(myGenepix6Files, columns=list(Rf='F635 Median',
> >Gf='F532 Median', Rb = 'B635 Median', Gb='B532 Median'), ...)
> >
> >Also, there are other arguments (other.columns) in the function for
> >reading more columns from the file.
> >
> >Hope it helps. Best,
> >
> >Saroj
> >
> >Ye, Bin wrote:
> >
> > >Hi,
> > >
> > >When I try to read the GenePix output file from GenePix 6, I got an
> > error as below:
> > >
> > >Error in "[.data.frame"(obj, , columns[[a]]) :
> > >        undefined columns selected
> > >
> > >I suspect GenePix 6 have some new columns different than previous version:
> > >
> > >Block  Column  Row     Name    ID      X       Y       Dia.    F635
> > Median     F635 Mean       F635 SD F635 CV B635    B635 Median     B635
> > Mean       B635 SD B635 CV % > B635+1SD    % > B635+2SD    F635 %
> > Sat.     F532 Median     F532 Mean       F532 SD F532 CV B532    B532
> > Median     B532 Mean       B532 SD B532 CV % > B532+1SD    % >
> > B532+2SD    F532 % Sat.     Ratio of Medians (635/532)      Ratio of
> > Means (635/532)        Median of Ratios (635/532)      Mean of Ratios
> > (635/532)        Ratios SD (635/532)     Rgn Ratio (635/532)     Rgn R2
> > (635/532)        F Pixels        B Pixels        Circularity     Sum of
> > Medians (635/532)        Sum of Means (635/532)  Log Ratio
> > (635/532)     F635 Median - B635      F532 Median - B532      F635 Mean -
> > B635        F532 Mean - B532        F635 Total Intensity    F532 Total
> > Intensity    SNR 635 SNR 532 Flags   Normalize       Autoflag
> > >
> > >Can anybody help me out? We need to deal with GenePix data for our
> > experiment.
> > >
> > >Thanks in advance!
> > >
> > >
> > >Bin